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Yorodumi- PDB-6ud0: Solution-state NMR structural ensemble of human Tsg101 UEV in com... -
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-Basic information
Entry | Database: PDB / ID: 6ud0 | ||||||
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Title | Solution-state NMR structural ensemble of human Tsg101 UEV in complex with K63-linked diubiquitin | ||||||
Components |
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Keywords | CELL CYCLE / ESCRT-I / viral budding / ubiquitin E2 variant | ||||||
Function / homology | Function and homology information positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway ...positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / viral budding / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / Flemming body / hypothalamus gonadotrophin-releasing hormone neuron development / virion binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / endosome to lysosome transport / female gonad development / negative regulation of epidermal growth factor receptor signaling pathway / seminiferous tubule development / male meiosis I / viral budding via host ESCRT complex / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / autophagosome maturation / viral release from host cell / regulation of proteasomal protein catabolic process / energy homeostasis / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / keratinocyte differentiation / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / multivesicular body / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / HCMV Late Events / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Strickland, M. / Watanabe, S. / Bonn, S.M. / Camara, C.M. / Fushman, D. / Carter, C.A. / Tjandra, N. | ||||||
Citation | Journal: Structure / Year: 2021 Title: Tsg101/ESCRT-I Recruitment Regulated by the Dual Binding Modes of K63-Linked Diubiquitin Authors: Strickland, M. / Watanabe, S. / Bonn, S.M. / Camara, C.M. / Fushman, D. / Carter, C.A. / Tjandra, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ud0.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ud0.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6ud0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/6ud0 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/6ud0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8604.845 Da / Num. of mol.: 1 / Mutation: K63R Source method: isolated from a genetically manipulated source Details: Distal domain of K63-linked diubiquitin. The K63R mutation is made to prevent formation of polyubiquitin during enzymatic linkage to the proximal domain. Joined to the proximal domain of ...Details: Distal domain of K63-linked diubiquitin. The K63R mutation is made to prevent formation of polyubiquitin during enzymatic linkage to the proximal domain. Joined to the proximal domain of diubiquitin at residue G76 using an isopeptide bond. Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0CG47 |
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#2: Protein | Mass: 8691.918 Da / Num. of mol.: 1 / Mutation: +D77 Source method: isolated from a genetically manipulated source Details: Proximal domain of K63-linked diubiquitin. The additional aspartic acid on the C-terminus (+D77) is made to prevent formation of polyubiquitin during enzymatic linkage to the distal domain. ...Details: Proximal domain of K63-linked diubiquitin. The additional aspartic acid on the C-terminus (+D77) is made to prevent formation of polyubiquitin during enzymatic linkage to the distal domain. Joined to the distal domain of diubiquitin at residue K63 using an isopeptide bond. Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0CG47 |
#3: Protein | Mass: 16633.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TSG101 / Plasmid: pET-28B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q99816 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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